Accelerating molecular dynamics simulations with MPI and GPU

In this article, we will explore techniques for speeding up molecular dynamics simulations with the help of HPC. We'll be focusing on utilizing NAMD as our simulation software and examining the ApoA1 in a water box environment.

Molecular dynamics simulation

Molecular dynamics simulation is a computational technique used to study the movements and interactions of atoms and molecules over time. By simulating the behavior of these particles, scientists can gain insights into various phenomena, such as protein folding, chemical reactions, and material properties.

Molecular dynamics simulations are computationally intensive and require significant computational resources. This makes them an excellent candidate for acceleration using High-Performance Computing (HPC). By harnessing the power of HPC, researchers can significantly reduce simulation time and tackle more complex and realistic systems. This acceleration allows for faster data analysis, improved understanding of molecular behavior, and enables scientists to make discoveries more efficiently.